Pharmaceutical composition and method for identifying a cancerous and/or an inflammatory disease in a patient

ABSTRACT

The invention relates to a method for treating a cancerous and/or an inflammatory disease in a patient, comprising internally administering to the patient an effective amount of a pharmaceutical preparation blocking the biological activity of at least one protein cluster (CMP) or group of CMPs containing at least CD26 and/or CD29. The invention also relates to a pharmaceutical composition for the treatment of a cancerous and/or an inflammatory disease in a patient, a method for identifying a cancerous and/or an inflammatory disease in a patient, a method of identifying at least one candidate for development of anti-cancerous or anti-inflammatory agents, a use of an antibody for preparing a pharmaceutical preparation or medicament for the treatment of prostate cancer, a composition or kit comprising at least one antibody and/or at least one ligand, and a biochip.

FIELD OF THE INVENTION

The invention relates to a method for treating a cancerous and/or aninflammatory disease in a patient, a use of a pharmaceutical preparationblocking the biological activity of at least one protein cluster (CMP)or group of CMPs, a pharmaceutical composition for the treatment of acancerous and/or an inflammatory disease in a patient, a method foridentifying a cancerous and/or an inflammatory disease in a patient, amethod of identifying at least one candidate for development ofanti-cancerous or anti-inflammatory agents, a use of an antibody forpreparing a pharmaceutical preparation or medicament for the treatmentof prostate cancer, a composition or kit comprising at least oneantibody and/or at least one ligand, and a biochip.

BACKGROUND OF THE INVENTION

Among the non-cutaneous malignant neoplasm prostate cancer is the mostcommon one in men in western countries. The disease accounts for thedeaths of approx. 30,000 men per year in the USA. The pathogenesis ofprostate cancer is unclear, although it was suggested that chronicinflammation is involved in the carcinogenesis. In the drive to findaltered molecular pathways in the process of prostatic carcinogenesis,proteomics techniques have been applied to identify multiple changes inprotein abundances simultaneously. In a recent study hundreds ofproteins were found to be up-regulated in prostate cancer (TNM stagesT1-T3), and dozens were found to be downregulated. Many of theseproteins were suggested to account for aberrant behaviour of multiplesignalling pathways in prostate cancer. An important question remains tobe answered: Where are specific pathways and their networks located insitu and how are they structured? A proteomic technology addressingthese features directly must be (i) non-destructive, (ii) able tovisualize a large number of different molecular cell components (MCC)(preferentially proteins) simultaneously, and (iii) alignable withhistological structures that can be readily examined in routinediagnostics working on light microscopic scales. The same considerationsalso apply to other cancerous and inflammatory diseases.

It is an object of the invention to ameliorate the identification andtreatment of cancerous and/or inflammatory diseases.

SUMMARY OF THE INVENTION

The foregoing object is inventively achieved by a method according toclaim 1 for treating a cancerous and/or an inflammatory disease in apatient. The object is also achieved through the uses of apharmaceutical preparation blocking the biological activity of at leastone protein cluster (CMP) or group of CMPs, a pharmaceutical compositionaccording to claim 8 for the treatment of a cancerous and/or aninflammatory disease in a patient, a method according to claim 13 foridentifying a cancerous and/or an inflammatory disease in a patient, amethod according to claim 17 of identifying at least one candidate fordevelopment of anti-cancerous or anti-inflammatory agents, the use of anantibody for preparing a pharmaceutical preparation or medicament forthe treatment of prostate cancer, a composition or kit according toclaim 21, and a biochip according to claim 24.

Advantageous embodiments with expedient further developments of theinvention are indicated in the corresponding subclaims.

An inventive method for treating a cancerous and/or an inflammatorydisease in a patient comprises internally administering to the patientan effective amount of a pharmaceutical preparation blocking thebiological activity of at least one protein cluster (CMP) or group ofCMPs containing at least CD26 and/or CD29. CD26 and CD29 in this contextare cell surface molecules that can be identified via the so-called“cluster of differentiation” or “cluster of designation” (abbreviated asCD) protocol. A protein cluster within the scope of the presentdisclosure is to be taken as combinatorial molecular phenotypes (CMPs)describing colocated and/or anti-colocated CDs, proteins and/ormolecules in a certain place of a cell. Accordingly, groups of CMPsrepresent regions of colocated and/or anti-colocated CDs, proteinsand/or molecules in a cell. The CMPs in this connection may for instancebe indicated in the form of a binary code, with it being possible toencode via any digit of the binary number (i.e. via any “bit”) whether apredetermined protein/molecule is given in a certain place of the cellor in a concentration exceeding a certain limit value (1 or True), orelse is not given in this place of the cell or only in a concentrationfalling short of a predetermined limit value (0 or False). The inventionis based on the insight that CD26 and/or CD29 within the context ofcancerous and/or inflammatory diseases are so-called “lead proteins”. Ona high level of molecular cell organization, protein clusters arefrequently interlocked as protein cluster networks (corresponding tosaid CMP motifs), which are controlled by said lead proteins: when thelead protein is inhibited, the clusters disassemble leading to loss offunction. Therefore the cancerous and/or an inflammatory disease caneffectively and without side-effects be cured by administering to thepatient an effective amount of said pharmaceutical preparation blockingthe biological activity of at least one protein cluster (CMP) or groupof CMPs containing at least CD26 and/or CD29. In its most simpleembodiment the pharmaceutical preparation used in the inventive methodcan be designed to block the biological activity of a CMP consisting ofCD26 and/or CD29 only. A protein cluster or protein group (CMP) blockedby means of the inventive method besides CD26 and/or CD29 may inprinciple also comprise further CDs, proteins and/or molecules, forexample one or more CDs and molecules as listed in the SupplementaryTable (see Annex).

In a further aspect of the invention the patient is a human and/or ananimal. In this context it has proven to be advantageous if saidpharmaceutical preparation is designed to be type and/orspecies-specific.

In a further aspect of the invention the disease is prostate cancer. Inthis case the treatment of the patient with the pharmaceuticalpreparation—which is blocking the biological activity of the at leastCD26 and/or CD29 comprising CMPs—has turned out to be particularlyeffective.

In a further aspect of the invention the pharmaceutical preparation isadministered if a protein cluster (CMP) or a group of CMPs alsocontaining CD44 and/or CD54 and/or CD138 and lacking at least one ofCD3, CD4, CD8, CD10, CD13, CD19, CD20, CD38, CD49d, CD58, and CD80 isidentified on cell surfaces of cells obtained from an affected part ofthe body of the patient. In this way a particularly effective treatmentof the cancerous and/or an inflammatory disease is ensured, so that inmost cases it is sufficient to treat the patient with a low dose of thepharmaceutical preparation. The protein cluster or protein group (CMP)in principle may also lack several or all CDs form the group of CD3,CD4, CD8, CD10, CD13, CD19, CD20, CD38, CD49d, CD58, and CD80.

In a further aspect of the invention said cells are obtained from atissue block and/or a single tissue section, the tissue being removedfrom the prostate of the patient. This allows for a particularly simpleand reliable test for the presence of the previously described CMPs andfor the presence of prostrate cancer.

The invention in another aspect relates to a use of a pharmaceuticalpreparation blocking the biological activity of at least one proteincluster (CMP) or group of CMPs containing at least CD26 and/or CD29 forthe treatment of a cancerous and/or an inflammatory disease in a patientby internally administering to the patient suffering such disease thepharmaceutical preparation in accordance with the method of any of thepreceding claims. The invention is based on the insight that CD26 and/orCD29 within the context of cancerous and/or inflammatory diseases areso-called “lead proteins”. On a high level of molecular cellorganization, protein clusters are frequently interlocked as proteincluster networks (corresponding to said CMP motifs), which arecontrolled by said lead proteins: when the lead protein is inhibited,the clusters disassemble leading to loss of function. Therefore thecancerous and/or an inflammatory disease can effectively and withoutside-effects be cured by use of said pharmaceutical preparation. In itsmost simple embodiment a pharmaceutical preparation can be used thatblocks the biological activity of a CMP consisting of CD26 and/or CD29only. A protein cluster or protein group (CMP) to be blocked by means ofthe pharmaceutical preparation may besides CD26 and/or CD29 in principlealso comprise further CDs, proteins and/or molecules, for example one ormore CDs and/or molecules as listed in the Supplementary Table (seeAnnex).

The invention in another aspect relates to a use of a pharmaceuticalpreparation blocking the biological activity of at least one proteincluster (CMP) or group of CMPs containing at least CD26 and/or CD29 forthe preparation of a medicament for the treatment of a cancerous and/oran inflammatory disease in a patient. The invention is based on theinsight that CD26 and/or CD29 within the context of cancerous and/orinflammatory diseases are so-called “lead proteins”. On a high level ofmolecular cell organization, protein clusters are frequently interlockedas protein cluster networks (corresponding to said CMP motifs), whichare controlled by said lead proteins: when the lead protein isinhibited, the clusters disassemble leading to loss of function.Therefore the cancerous and/or an inflammatory disease can beeffectively and without side-effects be cured by a medicament comprisingsaid pharmaceutical preparation. In its most simple embodiment themedicament may be designed to block the biological activity of a CMPconsisting of CD26 and/or CD29 only. A protein cluster or protein group(CMP) to be blocked by means of the medicament besides CD26 and/or CD29in principle may also comprise further CDs, proteins and/or molecules,for example one or more CDs and/or molecules as listed in theSupplementary Table (see Annex).

Another embodiment of the invention provides a pharmaceuticalcomposition for the treatment of a cancerous and/or an inflammatorydisease in a patient comprising a pharmaceutical preparation blockingthe biological activity of at least one protein cluster (CMP) or groupof CMPs containing at least CD26 and/or CD29. The invention in thisregard is based on the insight that CD26 and/or CD29 within the contextof cancerous and/or inflammatory diseases are so-called “lead proteins”.On a high level of molecular cell organization, protein clusters arefrequently interlocked as protein cluster networks (corresponding tosaid CMP motifs), which are controlled by said lead proteins: when thelead protein is inhibited, the clusters disassemble leading to loss offunction. Therefore the cancerous and/or an inflammatory disease caneffectively and without side-effects be cured by use of saidpharmaceutical preparation. In its most simple embodiment thepharmaceutical preparation may be designed to block the biologicalactivity of a CMP consisting of CD26 and/or CD29 only. A protein clusteror protein group (CMP) to be blocked by means of the pharmaceuticalpreparation may besides CD26 and/or CD29 in principle also containfurther CDs, proteins and/or molecules, for example one or more CDsand/or molecules as listed in the Supplementary Table (see Annex).

In a further aspect of the invention, the cancerous disease to betreated is prostate cancer. In this case the pharmaceuticalpreparation—which is blocking the biological activity of the at leastCD26 and/or CD29 comprising CMPs—has proven to be particularlyeffective.

In a further aspect of the invention, said pharmaceutical preparationcomprises an antibody, preferably a monoclonal antibody, and/or aprotein cross-linking agent and/or at least one of TSPAN4, CD9, Filamin,FLNB, CD81, CD46, MAP4K4, FHL2, NME1, PKC alpha, YWHAB, ITGB1BP1, LGALS8and GNB2L1. This facilitates a particularly specific blocking of thebiological activity of the at least one protein cluster (CMP) or groupof CMPs. Moreover, the pharmaceutical preparation is also low inside-effects.

In another aspect of the invention, the pharmaceutical preparationcomprises a pharmaceutically acceptable carrier. In the presentinvention, the pharmaceutically acceptable carrier depends on theconcrete design of the pharmaceutical composition. A person skilled inthe art can determine directly which pharmaceutically acceptable carriercan be used in the present invention. In one preferred embodiment, thepharmaceutically acceptable carrier is selected from physiologicalsaline. The amount of the pharmaceutically acceptable carrier isgenerally from 0.1% by weight to 99.9% by weight, preferably from 5% byweight to 95% by weight, more preferably from 40% by weight to 90% byweight, and most preferably from 60% by weight to 80% by weight.

In another aspect of the invention, the pharmaceutical preparation isformulated for oral, parenteral, intravenous, intramuscular, buccal,transdermal or transmucosal route of administration, in immediaterelease form or in controlled release form. In this way thepharmaceutical preparation can be administered in a particularlyflexible way and can be optimally adapted to the disease to be treated.

The invention in a further aspect relates to a method for identifying acancerous and/or an inflammatory disease in a patient comprising atleast the step of examining if at least a protein cluster (CMP) or agroup of CMPs containing at least CD26 and/or CD29 can be identified onthe cell surfaces of cells from a part of the body of the patient,wherein said part is suspected to be affected by said disease. Theinvention in this regard is based upon the insight that CD26 and/or CD29within the context of cancerous and/or inflammatory diseases areso-called “lead proteins”. On a high level of molecular cellorganization, protein clusters are frequently interlocked as proteincluster networks (corresponding to said CMP motifs), which arecontrolled by said lead proteins: when the lead protein is inhibited,the clusters disassemble leading to loss of function. Therefore, theinventive method allows for easy and reliably identification of acancerous and/or an inflammatory disease. In its most simple embodimentthe method according to the invention it may be tested for the presenceof a CMP consisting of CD26 and/or CD29 only. In principle, though, itmay also be tested for CMPs comprising besides CD26 and/or CD29 alsofurther CDs, proteins and/or molecules, for example one or more CDsand/or molecules as listed in the Supplementary Table (see Annex).

In another aspect of the invention, at least one protein cluster (CMP)or group of CMPs also containing CD44 and/or CD54 and/or CD138 andlacking at least one of CD3, CD4, CD8, CD10, CD13, CD19, CD20, CD38,CD49d, CD58, and CD80 is identified on the cell surfaces of said cells.This represents a reliable indication of the presence of a cancerousand/or an inflammatory disease such as prostate cancer.

In another aspect of the invention, at least one protein cluster (CMP)or group of CMPs lacking at least one of CD3, CD4, CD8, CD10, CD13,CD19, CD20, CD38, CD49d, CD58, CD80, CD44, CD54, and/or CD138 isidentified on the cell surfaces of said cells. This represents aparticularly reliable indication of the presence of a cancerous and/oran inflammatory disease such as prostate cancer. The protein cluster orprotein group (CMP) in principle may also lack several or all CDs formthe group of CD3, CD4, CD8, CD10, CD13, CD19, CD20, CD38, CD49d, CD58,CD80, CD44, CD54, and/or CD138. A reliable indication of the presence ofa cancerous and/or an inflammatory disease such as prostate cancer isgiven in further development of the invention in that the CMP is lackingat least CD44 and/or CD54 and/or CD138.

In another aspect of the invention, the disease is identified asprostate cancer if the cells derive from stroma and/or neoplasticepithelium of acini of prostate tissue and/or if at least 70%,preferably at least 75%, of the CMPs on the cell surface of at least onecell contain CD26 and/or CD29 and/or if at least 20%, preferably atleast 35%, of the CMPs on the cell surface of at least one cell compriseCD26 and/or CD29 and lack at least CD3, CD4, CD8, CD10, CD13, CD19,CD20, CD38, CD49d, CD58, and CD80. In this way prostate cancer can beidentified in a particularly simple and reliable way in the patientconcerned.

Another embodiment of the invention provides a method of identifying atleast one candidate for development of anti-cancerous oranti-inflammatory agents, comprising at least the step of examining ifat least one protein cluster (CMP) or a group of CMPs containing atleast CD26 and/or CD29 can be identified on the cell surfaces of cellsfrom a part of the body of the patient, wherein said part of the body issuspected to be affected by a cancerous and/or inflammatory disease. Theinvention in this regard is based on the insight that CD26 and/or CD29within the context of cancerous and/or inflammatory diseases areso-called “lead proteins”. On a high level of molecular cellorganization, protein clusters are frequently interlocked as proteincluster networks (corresponding to said CMP motifs), which arecontrolled by said lead proteins: when the lead protein is inhibited,the clusters disassemble leading to loss of function. Therefore, theinventive method allows for easy and reliably identification of saidcandidate for development of agents directed against the cancerousand/or inflammatory disease said part of the body is affected by. In themost simple embodiment of the method according to the invention, it istested for the presence of a CMP consisting of CD26 and/or CD29 only. Inprinciple, though, it may also be tested for CMPs comprising besidesCD26 and/or CD29 further CDs, proteins and/or molecules, for example oneor more CDs and/or molecules as listed in the Supplementary Table (seeAnnex).

In another aspect of the invention, said part of the body is prostatetissue and the disease is prostate cancer.

In another aspect of the invention, at least one protein cluster (CMP)or group of CMPs also containing CD44 and/or CD54 and/or CD138 andlacking at least one of CD3, CD4, CD8, CD10, CD13, CD19, CD20, CD38,CD49d, CD58, and CD80 is identified on the cell surfaces of said cells.This allows for a particularly reliable identification of a patientsuffering from prostate cancer.

The invention in a further aspect relates to a use of a human and/oranimal antibody, preferably a monoclonal antibody, directed against atleast CD26 and/or CD29 for preparing a pharmaceutical preparation ormedicament for the treatment of prostate cancer. As CD26 and/or CD29—ashas already been set out before—in the context of prostate cancer are“lead proteins”, the use of an antibody according to the inventionfacilitates a treatment that is particularly specific and thus low inside-effects. In this connection in dependency on the species and typeof the patient to be treated, a species-specific antibody can beselected, in order to avoid rejection reactions through the immunesystem. In principle one or more polyclonal, monoclonal, and/orrecombinant antibodies may be used. Further, it may in principle beprovided that at least one antibody also binds to CMPs comprisingbesides CD26 and/or CD29 also further CDs, proteins and/or molecules,for example one or more CDs and/or molecules as listed in theSupplementary Table (see Annex).

Another embodiment of the invention provides a composition or kitcomprising at least one antibody and/or at least one ligand wherein theantibody and/or ligand binds at least one cell surface protein selectedfrom the group of CD3, CD4, CD8, CD10, CD13, CD19, CD20, CD26, CD29,CD38, CD44, CD49d, CD54, CD58, CD80 and CD138 and wherein the antibodyand/or ligand is coupled with a label. The composition or kit can beused in one of the aforementioned methods. The composition or kit canalso comprise propidium iodide or the like for localizing cell nuclei.

In another aspect of the invention, at least one label is a fluorescentdye, quantum dot, radioactive tag, spin label, binding tag for a secondantibody and/or an enzyme. This allows for a flexible adaptation of thecomposition or kit to various applications and detection methods.

In another aspect of the invention, the composition or kit may bedesigned for use in a method for identifying a cancerous and/or aninflammatory disease in a patient.

Another embodiment of the invention provides a biochip for use in amethod according to any of the preceding embodiments wherein at leastone surface of the biochip comprises antibodies and/or ligands bindingto a protein cluster (CMP) or a group of CMPs of cell surfaces of humanand/or animal cells, wherein the CMP contains at least CD26 and/or CD29.In this regard the invention is based on the insight that CD26 and/orCD29 in the context of cancerous and/or inflammatory diseases are “leadproteins”. On a high level of molecular cell organization, proteinclusters are frequently interlocked as protein cluster networks(corresponding to said CMP motifs), which are controlled by said leadproteins: when the lead protein is inhibited, the clusters disassembleleading to loss of function. Therefore, the inventive biochip allows foreasy and reliably identification of a cancerous and/or an inflammatorydisease. In the most simple embodiment/design of the biochip accordingto the invention at least one surface may comprise antibodies and/orligands, by means of which it can be tested for the presence of a CMPconsisting of CD26 and/or CD29 only. In principle at least one surfaceof the biochip may be equipped with antibodies and/or ligands in such away that it can also be tested for CMPs comprising besides CD26 and/orCD29 further CDs, proteins and/or molecules, for example one or more CDsand/or molecules as listed in the Supplementary Table (see Annex).

In another aspect of the invention, at least one surface of the biochipcontains antibodies and/or ligands binding to a protein cluster (CMP) ora group of CMPs of cell surfaces of human and/or animal cells, whereinthe CMP contains at least one of CD3, CD4, CD8, CD10, CD13, CD19, CD20,CD38, CD44, CD49d, CD54, CD58, CD80 and CD138. In this way for theidentification of cancerous and/or inflammatory diseases important cellmarkers can be tested by means of the biochip according to theinvention, so that a particularly fast and reliable diagnosis isfacilitated.

Further features of the invention derive from the claims, theembodiments, as well as the drawings and tables. The features andfeature combinations previously mentioned in the description as well asthe features and feature combinations mentioned in the following in theembodiments can be used not only in the combination indicated in eachcase, but also in all other combinations or individually, withoutleaving the scope of the invention. It is shown in:

FIG. 1 a schematic illustration of the topological hierarchies ofproteins within a toponome;

FIG. 2 mappings of molecular cell components (MCC) by MELC/TIS running 9incubation-imaging-bleaching cycles on a single fixed tissue section.

FIG. 3 a toponome map showing the location of the 30 most frequent outof more than 2,000 different CMPs detected in the visual field of FIG.2;

FIG. 4 mappings of molecular cell components by MELC/TIS inside andaround a prostate acinus and in the surrounding stroma;

FIG. 5 an illustration of the 41 most frequent out of more than 2,100different CMPs in the area shown in the MELC/TIS cycle map of FIG. 4;

FIG. 6 an illustration of the selective expression of CMP1 insubcellular sites of neoplastic prostate acini; and

FIG. 7 a scheme illustration of the major features of the networksformed by 17 different cell surface proteins, and functional annotationof these networks to specific cell types in prostate cancer.

The microscopic fluorescence robot technology MELC/TIS is capable ofimaging at least 100 different molecular cell components (MCCs) in onecell or tissue section. Multi-Epitope-Ligand-Cartography (MELC)/toponomeimaging system (TIS) overcomes the spectral limitation of traditionalfluorescence microscopy by using large dye-conjugated tag libraries andautomatically bleaching a dye after imaging and re-labelling the same oranother MCC in the identical sample with the same dye coupled to a taghaving the same or another specificity, and repeat similar cycles withother tags for multiple times revealing multidimensional colocationpatterns. By this approach, the so called toponome (the functionalprotein networks, or, the biological code of the cell) of a cell can begathered. After the first description of the technology in 1990, therelevance of this approach to cell function has been increasinglyrecognized.

The MELC/TIS technology is unparalleled when it comes to thecolocalization of a very large number of proteins using microscopy. Theability to colocalize proteins on a large scale is regarded as abottleneck in the drive to understand how proteomes are organized inindividual cells, and how interlocked clusters of proteins exert controlover cellular functions. In the following examples MELC/TIS was used forthe analysis of prostate tissue. By cyclical imaging of 17 differentMCCs, 16 of which were cell surface proteins, the resultinghigh-dimensional protein colocation and anti-colocation code isdescribed. Also, cell type specific protein clusters are visualized, anda protein cluster motif that is selectively expressed by neoplasticepithelial cells inside prostate acini is demonstrated.

Material and Methods

Specimen. A single tissue was cut from a prostate tissue block ofradical prostatectomy (61 yr old man with lymph node metastasis andhistologically confirmed prostate cancer). The tissue block was removedfrom the peripheral zone of the prostate, containing multicentric fociof cancerous prostate acini and acini with features of low grade andhigh grade intraepithelial neoplasia (PIN).

Tag library. The tags used to label proteins and ligands in the tissuesection, assembled as a toponome mapping library (MELC/TIS tag library),are summarized in Table 1. Table 1 shows a list of molecular cellcomponents labelled in the following examples (column 1) together withtheir locus link annotations (columns 2 and 3) and the correspondingincubation imaging bleaching cycles (column 4). Column 3 gives some ofthe known cellular expressions and functions of the moleculesillustrating why they were selected for the TIS procedure searching fortheir topological assemblies. The tags used for cyclical imagingprocedures were either conjugated to FITC or PE, and signals of two tagsper cycle were imaged. The molecules selected for the toponome imagingprocedures in this study are all reference markers of the cell surface,which have all been calibrated for MELC/TIS in an earlier study. Some ofthe known cellular expressions and functions of these molecules arelisted in column 3 of table 1 illustrating why these molecules werechosen for the TIS procedure.

Preparation of the tissue section. A five μm thick tissue section wascut from the prostate tissue block in a cryotome at −15° C. and placedon a large cover slip as described. The section was then fixed inacetone at room temperature (RT) for 10 seconds, air dried and stored at−80° C. until use. Before use (see MELC/TIS below), the section wasagain fixed in acetone (at −20° C.) for 10 min, air dried, and thenrehydrated in PBS at RT. This was followed by incubation with normalgoat serum for 30 min, and a washing step with PBS.

Optical parameters. To obtain an overview at 2D on the many cell typesand their phenotypic variations present in the tissue, an optical set upwas chosen, that was already successfully applied for the detection ofprotein clusters in other biological samples. For the MELC/TISexperiments (see below) a 16× oil objective with a numerical aperture of0.5 was applied giving a pixel dimension of 850 nm×850 nm (=0.7225 μm)by using a two fold binning.

MELC/TIS. The features and functionalities of a MELC/TIS imaging robothave been described earlier. The procedure to run repetitive incubationimaging bleaching cycles (RIIBC) on the tissue section was as follows.

In brief, the cover slip with the tissue section (above) was placed onthe stage of an inverted wide-field fluorescence microscope (Zeiss)equipped with fluorescence filters for fluoresceine-iso-thio-cyanate(FITC) and phycoerythrin (PE) (filter sets for FITC: excitation 480/40BP; beam splitter 505 LP; emission 527/30 BP; filter sets for PE:excitation 546/11 BP; beam splitter 560 LP; emission 585/40 BP). For thecyclical imaging procedures, a given FITC- and PE-conjugated tag wasmerged in one cycle (Table 1, column on the right). Altogether 9 cycleswere performed. Fluorochrome-labelled tags and wash solutions were addedand removed robotically under temperature control (20° C.), avoiding anydisplacement of the sample and objective. In each cycle, two differenttags, conjugated to either FITC or PE, were added (cycle sequence seetable 1); phase contrast and fluorescence images were acquired by ahigh-sensitivity cooled CCD camera; the sample was washed with PBS andbleached at the excitation wavelengths; and post-bleaching phasecontrast and fluorescence images were acquired. Data acquisition wasfully automated using home made software. Note that interference ofantibodies was avoided by permuting the cycle position of antibodies foroptimal labelling results during the calibration procedure preceding thedefinitive measurements. The definitive sequence of cycles andmolecules/proteins labelled per cycle is given in table 1. Thesensitivity of the approach ranges between 500 and several thousandcopies of the molecules labelled per cell, depending on the avidity ofthe used tags. Since monoclonal CD antibodies used in this study areextremely well characterized for their specificity in diagnosticmedicine, we expect that positive signals indeed represent the moleculesof interest. Hence false positive results can be excluded. We can notexclude that tissue sites, in which no signal is seen, do not containthe molecule of interest, which can be due to epitope masking resultingfrom conformational changes or binding of the corresponding epitope tointeracting proteins.

Construction of a two-dimensional toponome map. Fluorescence images,produced by each tag, were aligned pixel-wise using the phase contrastimages, with an in-register accuracy of +/−one pixel. Fluorescent pixelswere then parsed by regarding the list of fluorescence intensities I₁,I₂, I₃ . . . I_(n) for proteins 1, 2, 3 . . . n in any particular pixelor voxel as the values of an n-dimensional vector associated with thatpixel. This vector can then be binarized by selecting thresholds T₁, T₂,T₃ . . . T_(n) for proteins 1, 2, 3 . . . n, and setting the vectorvalues for any protein m to zero if I_(m)<T_(m) and to 1 if not, usingthresholds manually set by human experts from within an automaticallygenerated range. The binarized images were then combined to form a listof combinatorial molecular phenotypes (CMPs) representing theproteins/molecules expressed in each pixel, or groups of CMPsrepresenting regions of interest. Given CMPs (protein clusters) orgroups of CMPs were visualized in false colours at their location. Wehave established these steps in home made software, termed MoPPi(Modular Processing Pipeline).

Each signal within a CMP is mapped as tag present (=1) or tag absent(=0), depending on whether the value for the fluorescence signal isabove or below this threshold, respectively (=1 bit information perprotein at a pixel/voxel). CMPs assembled as a group will have uniquefeatures as defined by the assembly's lead proteins (L=1), absentproteins (A=anticolocated, 0) and wild card proteins (W=variablyoccurrence of a protein 0 and 1 in given CMPs of a CMP group). We definesuch CMP groups as a CMP motif (FIG. 1), denoting a given functionalregion of a cell or tissue. FIG. 1 shows a schematic illustration of thetopological hierarchies of proteins within the toponome. By using athree symbol code (LAW, FIG. 1), differences of cell states and celltypes can be readily identified in studies comparing large experiments,or, diseases with normal conditions. “L” means lead protein (common toall CMPs of a CMP motif), “A” means absent protein (absent in all CMPsof a CMP motif), and “W” means wild card proteins (proteins that arevariably associated with the (L) and the (A) proteins of a motif)(source: Ref 7).

In the present set up, with the optical parameters chosen (see materialand methods section), a pixel expressing a given CMP, or proteincluster, has a dimension of 0.7225 μm.

Results

Nine MELC/TIS cycles generate a gallery of 17 images. To illustrateworking of toponomics in prostate cancer analysis, we have chosen asingle tissue section of histologically verified prostatic cancerpresenting as acinus type, with multifocal variations including presenceof intraepithelial neoplasia (PIN). The results described henceforthwere obtained by using the robot system MELC/TIS for the imaging of thetoponome. To select a visual field for our study, a 16× oil phasecontrast/fluorescence objective was used. Once the visual field wasselected by an expert (FIG. 2 a), we started the fully automatedprocedure of cyclical imaging of 17 different affinity tags in theselected visual field (FIG. 2 b-r). This tag library had been calibratedby a procedure described by us previously. Interference of antibodieswas avoided by permuting the cycle position of antibodies for optimallabelling results during the calibration procedure preceding thedefinitive measurements. The definitive sequence of cycles andmolecules/proteins labelled per cycle is given in table 1. Thesensitivity of the approach ranges between 500 and several thousandcopies of the molecules labelled per cell, depending on the avidity ofthe used tags. Since the tags used in this study, especially themonoclonal CD antibodies are extremely well characterized in theliterature for their specificity of the molecules labelled in situ, weexpect that positive signals indeed represent the molecules of interest.Hence false positive results are very unlikely, while we can not excludethat tissue sites, in which no signal is seen, do not contain themolecule of interest, which can be due to epitope masking resulting fromconformational changes or binding of the corresponding epitope tointeracting proteins.

FIG. 2 generally shows mappings of molecular cell components (MCC) byMELC/TIS (tag library of table 1) running 9 incubation-imaging-bleachingcycles on a single fixed tissue section. FIG. 2 a shows phase contrastview followed by MELC/TIS maps of 17 proteins/molecules (shown in FIG. 2b-r). For specificity and selectivity of the labelled MCC see table 1.The prostate acinus denoted by an arrow in (r), is magnified in acorresponding gallery of images of FIG. 4 (Bar: 100 μm). As illustratedin FIG. 2, the imaging robot generated 17 single grey value imagesresulting from 9 different incubation-imaging-bleaching cycles. Tocorrelate our results with known markers for prostate cancerclassification, we have included antibodies against CD26 specificallyrecognizing prostate epithelium and CD138 as a marker for prostatecancer progression. As illustrated in FIG. 2 (j, r), these antibodiesselectively label prostate epithelium, which is in good agreement withearlier findings. Some of the tags (CD3, CD4, CD8, CD38) selectivelyrecognized cell structures in the fibrocollagenous stroma surroundingthe prostate acini (FIG. 2). Presence of CD4 and CD8 T lymphocytes(FIGS. 2 d, e, respectively) substantiates presence of abundantinflammatory cells. Other tags labelled both cell structures in thestroma and inside the epithelial acini, such as CD13, CD29, CD44, CD49d,CD54, CD58, and CD80 (FIGS. 2, g, k, m, n, o, p, q, respectively). Tolocalize cell nuclei, we have included propidium iodide in our imagingcycles (FIG. 2 b). CD₂₀ and CD19 as markers of B lymphocytes werenegative (FIG. 2 h, i, respectively). Interestingly, CD10 was present ina subset of epithelial cells inside some of the acini (FIG. 2 f).

Localization of protein clusters (CMPs). As described in the materialand methods section, we have applied our MoPPi software tool to (i)align the images from FIG. 2, (ii) set expert-selected thresholds forsignal binarization as described, and (iii) use our CMP extractionalgorithm to find all CMPs contained in the corresponding visual field.This procedure led to what we term a toponome map. Altogether wedetected 2,100 different mutually exclusive CMPs. Supplementary Table 1gives 165 CMPs in the order of their frequency (number of pixelsexpressing these CMPs) and shows the most frequent CMPs detected in thevisual field of FIG. 2. The CMPs are based on the combinatorial analysisper pixel of 16 different cell surface protein signals (table 1), thatdo not colocalize with propidium iodide signal. CMPs are sortedaccording to their pixel frequency (from top to bottom, high to low).

Table 2 shows a coding list of the 30 most frequent distinct CMPs (outof 2,100 in total) detected in the visual field of FIG. 2. The frequencyof a CMP is defined as the number of pixels in the visual field of FIG.2, which express this given CMP. Hence, each CMP is distinct from otherCMPs (compare the combinatorial 0/1 codes, horizontal lines in table 2);moreover, the pixels that express a given CMP, exclude expression of anyother distinct CMP, so that CMPs are, topologically, mutually exclusive.

The expression/location of these CMPs in the tissue is shown in FIG. 3as overlay with the CD138 fluorescence signal. In other words, FIG. 3illustrates the location of these CMPs by aligning their differentcolours (resp. grey scales) with the original CD138 fluorescence signal.The colours/grey scales for the distinct CMPs on the left correspond tothe colours indicating their location in FIG. 3. The column on the right(frequency) indicates the number of pixels that express the given CMP.Protein/molecule coding list (numbers in the top line): 1=propidiumiodide; 2=CD3; 3=CD4; 4=CD8; 5=CD10; 6=CD13; 7=CD19; 8=CD20; 9=CD26;10=CD29; 11=CD38; 12=CD44; 13=CD49d; 14=CD54; 15=CD58; 16=CD80;17=CD138. The range of CMP frequencies between 24.087 and 873 pixels(column on the right), with a cut off value at 873 pixels (correspondingto 30 different CMPs, column on the left) was chosen, becausefrequencies below 800 are difficult to detect visually in an image. Thisallowed for the examination by visualization, (i) which CMPs arerestricted to the CD138 positive epithelium of acini, (ii) which CMPsare confined to the stroma, and (iii) which CMPs are expressed by bothstroma and the epithelium.

Cell type specific protein clusters and protein cluster motifs. Toprovide a more detailed view of these CMP locations, a detail of FIG. 2(r, arrow) was depicted: acinus singled out by CD138. This detail isdisplayed as a selected gallery of the 17 images corresponding to the 9TIS cycles (FIG. 4). FIG. 4 shows mappings of molecular cell componentsby MELC/TIS inside and around a prostate acinus and in the surroundingstroma. The area corresponds to the detail of FIG. 2 (r, arrow). FIG. 4a shows a fluorescence signal of propidium iodide localizing cellnuclei; FIGS. 4 b-q show localizations of 16 different cell surfaceproteins specified in table 1. (Bar: 100 μm)

The most frequent CMPs of this area were then localized in differentcolours and as overlays with the CD138 fluorescence signal (FIGS. 5 b,c, d). FIG. 5 generally illustrates the 41 most frequent out of morethan 2,100 different CMPs in the area shown in the MELC/TIS cycle map ofFIG. 4: FIG. 5 a shows a fluorescence signal of CD138; FIG. 5 b shows 41most frequent CMPs displayed in different colours; FIG. 5 c shows afraction of the latter CMPs selectively expressed by cellular structuresin the stroma surrounding the acinus; and FIG. 5 d shows CMPs which areselectively expressed by a fraction of epithelial cells inside theacinus showing features of proliferative intraepithelial neoplasia(PIN). FIG. 5 d also shows irregular spacing and stratification of theinner secretory cells with cytoplasmic projections towards the lumen ofthe acinus (d, arrow 1); basal cell layer with partially inconspicuous(d, arrow 2), and partially discontinuous parts (d, arrow 3). The basalepithelial cells (d, arrow 2) displaying normal cell features do notexpress any of these CMPs.

The colour coding (resp. grey scale) list for CMPs of FIGS. 5 c and 5 dis given in Table 3 part I and part II, respectively: part I denotesCMPs which are selective for the stroma (FIG. 5 c), and part II givesthe CMPs selective for PIN cells (FIG. 5 d). The latter CMPs represent agroup that together are assembled as a CMP motif with CD26 and CD29 aslead proteins (compare table 3, part II; Bar: 100 μm.)

Table 3 (part I and part II) gives the corresponding colour or greyscale coding list of these CMPs. Table 3 part I shows a colour (resp.grey scale) coding list of the 25 most frequent CMPs (out of 2,100)which are selectively expressed by cell structures in the stromasurrounding neoplastic prostate acini. The CMPs are sorted according totheir frequency (from top to bottom, high to lower) and expression ofthese CMPs in the stroma is shown in FIG. 5 c as overlay with the CD138signal. Table 3 part II shows a colour (resp. grey scale) coding list ofthe 16 most frequent CMPs (out of 2,100) which are selectively expressedby cell structures in the neoplastic prostate acinus. The CMPs aresorted according to their pixel frequency (from top to bottom, high tolower). Expression of these CMPs in the acinus is shown in FIG. 5 d asoverlay with the CD138 signal.

In other words, FIG. 5 c and FIG. 5 d show those CMPs which arerestricted either to the stroma or the CD138 positive acinus,respectively. This acinus shows features of proliferativeintraepithelial neoplasia (PIN), as indicated (among other things) by(i) irregular spacing and stratification of the inner secretory cellswith cytoplasmic projections towards the lumen of the acinus (FIG. 5 d,arrow 1), and (ii) the basal cell layer with partially inconspicuous(FIG. 5 d, arrow 2), and partially discontinuous parts (FIG. 5 d, arrow3).

Notably, 25 CMPs are selectively expressed by cells in the stroma (Table3, part I; FIG. 5 c), and 16 CMPs (Table 3 part II; and FIG. 5 d) areunique for a fraction of epithelial cells displaying the features ofPIN. Interestingly, many of the basal epithelial cells, displayingCD138, do not express these CMPs (FIG. 5 d, arrow 2). This stronglysuggests that neoplastic cells and inconspicuous epithelial cells can bedistinguished by the CMPs shown in Table 3 (part II). Moreover, theseCMPs together represent a CMP group that fulfil the criteria of a CMPmotif (compare Table 3 part II with the scheme in FIG. 1): All CMPsshown in table 3 part II, have in common CD26 and CD29 as lead proteins(=L), while CD3/CD4/CD8/CD19/CD20/CD44/CD80, are absent (anti-colocated)in all these CMPs, and CD10/CD13/CD38/CD49d/CD54/CD58/CD138 are variablyassociated with the lead and anti-colocated molecules (=0). As shown anddescribed in detail for the human immune system and other cell systems,this gives a three symbol code (L, A, W) for protein clustersselectively associated with neoplastic cells in the present example(Table. 3 part II: CMP motif).

By following a strategy of extraction of the most prominent and relevantinformation contained in the many CMPs detected, each single CMP out ofthe 30 and 41 most frequent CMPs has been visualized. The CMPs aresummarized in Tables 2 and 3, and in supplementary table 1,respectively. As shown in table 3 (part II), the most frequent CMPswithin the PIN-CMP motif is CMP1 coexpressing the lead cell surfaceproteins CD29/CD26 together with CD54 and CD138, while all other 12 cellsurface proteins are anti-colocated (=0) in that CMP. This CMP is indeedexpressed in all except one of the acini undergoing neoplasia in thevisual field (FIG. 6).

FIG. 6 illustrates the selective expression of CMP1 in subcellular sitesof neoplastic prostate acini. CMP1 is the most frequent CMP within theCMP motif of table 3, part II. FIG. 6 a shows an overview with arrow 1and arrow 2 denoting apical sites of secretory cells, and arrow 3denoting cell projections at the basolateral site of an acinus. FIGS. 6b-c show details illustrating tissue sites denoted by arrows 1, 2 and 3,respectively. Note the circumscribed association of the CMP 1 (browncolour) with cell surface fluorescence signal of CD133 (white). “BE”means basal epithelial cell layer. (Bars: 6 a: 100 μm; 6 b-d: 10 μm.)

As indicated by arrows, the location of this CMP is interesting, becauseit singles out apical (FIG. 6 a, arrow 1, arrow 2) and/or basolateralsites of the secretory cells, or, epithelial cells which are close tothe basal membrane, or which have formed cell projections that mighthave penetrated the basal lamina border (FIG. 6 a, arrow 3). Hence,while this CMP is clearly present in most of the acini in the field, itis expressed selectively at subcellular sites of the epithelial cellswhich are suspicious for cancer progression (migration/invasion).

Another prominent feature of the tissue analyzed in the present exampleis the striking selectivity of CMPs for non-epithelial cellularstructures in the fibrocollagenous stroma surrounding the acini (FIG. 5c). Table 3 (part I) gives the colour coding list for these CMPs. Thesestructures could be classified as T lymphocytes (CD4 and CD8) (table 3part I, T4, and T8, respectively), capillary endothelium (CD29) (table 3part I, C), and other stromal cells which were not further characterized(S) (table 3 part I).

Together these major results are summarized in a scheme (FIG. 7)illustrating the cell type specific protein clusters in prostate tissue.FIG. 7 shows a scheme illustrating the major features of the networksformed by 17 different cell surface proteins (coding list, on the left),and functional annotation of these networks to specific cell types inprostate cancer. Networks are extracted from the toponome motifs shownin tables 1 through 3. Proteins co-mapped by MELC/TIS are arranged ascircles around cell type specific lead proteins; Solid dots representproteins, which are variably associated with the lead proteins(corresponding to the wild card proteins illustrated in FIG. 1); Emptydots represent proteins which are anti-colocated (=0 in FIG. 1). Leadproteins are encircled (very center of each network), and theirdifferential assembly with the wild card protein is symbolized by lines.Toponome motifs were only found for PIN-, CD4 lymphocytes and capillarycells, while stromal cells and CD8 lymphocytes did not show any motifwithin the most frequent CMPs of tables 1 through 3. Propidium iodide asDNA marker (number 1 in the molecule coding list) is omitted because ofits irrelevant information concerning cell surface protein clustering.

To sum up, these findings describe the feasibility to map a fraction ofthe cell surface toponome of proteins in a single tissue section in thisdisease. Accordingly, the present findings provide insight in proteinnetworks driving the disease. The present approach has led to entirelystructure-bound combinatorial data generating a new type ofhigh-dimensional data space. Mapping the organized proteome by MELC/TISin earlier studies revealed the structure-bound architecture offunctional protein networks (the toponome). It has unravelled newcellular mechanisms and lead proteins controlling pathogenic networks inrhabdomyosarcoma cells. By colocalizing 17 different molecularcomponents in one tissue sectionmore than 2,000 different proteinclusters (CMPs) were detected, some of which are specifically associatedas CMP motifs with the features of neoplasia (e.g. proliferativeintraepithelial neoplasia, PIN). Also, CMP motifs selectively associatedwith inflammatory CD4 lymphocytes and capillary endothelium weredetected. No specific motifs were found for stromal cells of thefibrocollagenous stroma surrounding prostate acini, and for inflammatoryCD8 lymphocytes, while both these latter cell types did express severalsingle marker proteins. Simple protein network graphs illustrate howthese distinct features of differentially associated proteins areselectively displayed by these cell types (FIG. 7).

These findings are in keep with our earlier observations, that CMPmapping rapidly leads to insight into relevant protein assemblies andthe rules of their topological order, to address what we term thegenerative grammar of the toponome. Detection of clear-cut cell-typespecific clustering of proteins in situ relies on the ability ofMELC/TIS to co-map a quasi random number of proteins by cyclical imagingin any given data point of a digitized image of a tissue section in oneprocedure. Compared to the localization of only one or few proteins,this leads to an exponential increase of biological information, asshown in the present invention. Protein clusters (differential localcombination of n proteins), rather than a single protein species,clearly distinguish cell types, subcellular sites, or, differentfunctional states of a cell or a tissue. Moreover, on an even higherlevel of molecular cell organization, protein clusters are frequentlyinterlocked as protein cluster networks (corresponding to CMP motifs),which are controlled by lead proteins: when the lead protein isinhibited, the clusters disassemble leading to loss of function. In thepresent invention a CMP motif has been found that is expressed insideprostate acini by epithelial cells with features of neoplasia (e.g.proliferative intraepithelial neoplasia, PIN) (PIN specific motif),while basal epithelial cells with inconspicuous features do not expressthis motif. This finding supports the toponome approach to new molecularpathways in prostate cancer.

First, the two lead proteins (CD29 and CD26) of the PIN-specific motifdetected here are structurally and functionally distinct: CD29 is a betaintegrin chain which associates as a heterodimer non-covalently with thealpha integrin chain subunit. The molecule is involved in cell-cell andcell-matrix interactions. The highly conserved cytoplasmic domain ofCD29 interacts with the cytoskeleton. CD26 (dipeptidyl peptidase IV,DPPIV), is a type II transmembrane integral protein. It is a cellsurface protease cleaving dipeptides from NH2-termini of proteinsprovided that the penultimate residue is proline. The distinct structureand function of these two proteins coexisting as lead proteins in allCMPs, or, protein clusters of the detected PIN motif, is consistent withour earlier observation in rhabdomyosarcoma cells, that supramolecularcell surface clusters are, by a rule, composed of highly dissimilarproteins.

Second, the detection of CD29 and CD26 and their corresponding motifsingles out these proteins as candidates for therapeutic intervention inprostate cancer. Therefore, a blockade of these proteins, for example bycross-linking agents, interferes with the control of these proteins overthe PIN motif, leading to its disassembly.

Third, the CMP motif clusters appear to be specific modules of the cellsurface of PIN cells: by interaction with the cytoskeleton, for examplethrough CD29, and through continuous proteolytic activity of CD26, thecluster is involved in PIN-specific cell polarization and migration. Anintervention on the level of these two proteins therefore interfereswith tumor progression. Given CD26 as a proteolytic lead protein enzyme,assembled with CD29 as an integrin in our present example, a newfunctional model emerges: cell surface enzymes are important leadelements interacting with cytoskeleton-linking proteins to exert controlover topology and function of extended protein cluster networks.

Together, finding of tumour specific targets or target clusters, andunderstanding the molecular mechanisms of disease in situ is a majorgoal in cancer research. High-throughput transcriptomics and proteomicsstudies, based on ex vivo analyses, have already assembled many newinformation on interesting target candidates, and efficient methods forhandling such high-dimensional data have been described. By contrast,the present invention addresses the architecture of protein networksdirectly in situ in the individual cell or tissue section. This leads toa different kind of high-dimensional data, with a topological mosaic ofprotein colocation and anti-colocation clusters. Construction ofcorresponding toponome reference maps of prostate cancer serves as thestarting point in the search of disease-specific protein networks andlead proteins. Such reference maps can be used as a scaffold, or,assembly of combinatorial molecular landmarks, for the construction ofmuch larger maps involving many more proteins.

The optical set up in the present study, with a pixel dimension of0.7225 μm, was chosen to address in one visual filed as many cells andacini as possible, with a sufficient resolution to find protein clustersassociated with cells and cell surfaces. However, if needed, the opticalresolution of MELC/TIS can be substantially enhanced for any kind ofanalysis pinpointing protein clusters in pixels with a dimension of atleast 0.0466 μm, as shown in detail in our earlier 2D and 3D studies.

The foregoing description of various aspects of the invention has beenpresented for purposes of illustration and description. It is notintended to be exhaustive or to limit the invention to the precise formdisclosed, and modifications and variations are possible. Suchmodifications and variations are intended to be included within thescope of the invention as defined by the accompanying claims. Theparameter values for the definition of processing and measuringconditions for the characterization of specific properties of thesubject matter of the invention are to be regarded as comprised withinthe scope of the invention also within the limits of deviations—e.g. dueto measuring errors, system errors, weighing errors, DIN tolerances andthe like indicated in the documents.

TABLE 1 Molecule/ MELC/ moity Official Cellular expression/ TIS robotrecognized symbol Known Function cycles CD4 [CD4] CD4 antigen (p44) isexpressed by cycle 1 PE MHC class II-restricted T cells and binds MHCclass II molecules, acting as co-receptor in recognition of foreignantigen [Homo sapiens] CD8 [CD8] CD8 antigen (alpha polypeptide, p32) iscycle 1 FITC expressed by MHC class I-restricted T cells and aco-receptor for MHC class I- restricted TCRs in antigen recognition[Homo sapiens] CD3 [CD3E] CD3E antigen (epsilon polypeptide, cycle 2 PETiT3 complex) is expressed by T cells and part of the TCR receptorcomplex. It is necessary for cell surface expression of TCR and forantigen recognition and signal transduction. [Homo sapiens] CD26 [DPP4]Dipeptidylpeptidase 4 (CD26, cycle 2 FITC adenosine deaminase complexingprotein2) is expressed by activated T cells and cleaves off N-terminalX-Pro or X-Ala dipeptides from polypeptides and is a costimulatorymolecule in T cell activation. [Homo sapiens] CD29 [ITGB1] Integrin,beta 1 (fibronectin receptor, cycle 3 PE beta polypeptide, antigen CD29includes MDF2, MSK12) is expressed by all leukocytes and formsheterodimers with many integrin α subunits which mediate cell-cell andcell-matrix adhesion. [Homo sapiens] CD49d [ITGA4] Integrin, alpha 4(antigen CD49D, alpha cycle 3 FITC 4 subunit of VLA-4 receptor) is anadhesion molecule of T and B cells and associates with β1 or β7. It isinvolved in lymphocyte migration, homing and rolling, and is acostimulatory molecule for T cell activation. [Homo sapiens] CD138[SDC1] Syndecan 1 is expressed by immature cycle 4 PE B cells and bearsboth heparin sulphate and chondroitin sulphate. It links thecytoskeleton to the interstitial matrix. [Homo sapiens] CD13 [ANPEP]alanyl (membrane) aminopeptidase cycle 4 FITC (aminopeptidase N,aminopeptidase M, microsomal aminopeptidase, CD13, p150) is expressed bygranulocytes and monocytes and their precursors. It cleaves single aminoacids from amino terminus of small peptides. It participates in trimmingpeptides bound to MHC class II molecules. [Homo sapiens] CD38 [CD38]CD38 antigen (p45) is expressed by cycle 5 PE early-stage B and T cellsand has multiple enzymatic activities. It plays possible signalling rolein cell activation, proliferation, apoptosis, due to modulation ofcytoplasmatic calcium fluxes and phosphorylation of key substrates.[Homo sapiens] CD44 [CD44] CD44 antigen is expressed by most cell cycle5 FITC types and is an adhesion molecule, which mediates leukocyteattachment to and rolling on endothelial cells, homing to peripherallymphoid organs and sites of inflammation. [Homo sapiens] CD54 [ICAM1]Intracellular adhesion molecule 1 cycle 6 PE (CD54) is expressed byactivated T and B cells and binds CD11a/CD18 (LFA-1) and CD11b/CD18(Mac-1), contributing to leukocyte extravasation from blood vessels.[Homo sapiens] CD58 [CD58] CD58 antigen (lymphocyte function- cycle 6FITC associated antigen 3) is expressed by many hematopoietic and non-hematopoietic cells and mediates the adhesion between killer T cells andtarget cells, antigen-presenting cells and T cells, thymocytes andthymic epithelial cells. [Homo sapiens] CD20 [MS4A1] Membrane-spanning4-domains, cycle 7 PE subfamily A, member 1 is expressed by B lineagecells and plays a possible role in regulation of B cell activation andproliferation. There is evidence for CD20 function as a B cell calciumchannel subunit. [Homo sapiens] CD10 [MME] Membranemetallo-endopeptidase cycle 7 FITC (neutral endopeptidase,enkephalinase, CALLA, CD10) is expressed by pre-B and pre-T cells and isa marker for common ALLs and certain lymphomas. It cleaves at the aminoside of hydrophobic residues and inactivates several bioactive peptides.[Homo sapiens] CD19 [CD19] CD19 antigen is expressed by B lineage cycle8 PE cells and is a critical signal transduction molecule that regulatesB cell development, activation and differentiation. It regulatesresponses, playing a dominant role in establishing signalling thresholdsfor antigen receptors and other surface receptors on B lymphocytes.[Homo sapiens] CD80 [CD80] CD80 antigen (CD28 antigen ligand 1, cycle 8FITC B7-1 antigen) is expressed by activated B and T cells. It isresponsible for Co- stimulation of T cell activation with CD86. It playsa potential role in autoimmune, humoral and transplant responses. [Homosapiens] Prop lig. — Propidium iodide is an intercalating cycle 9 agentand a fluorescent molecule, that can be used to stain DNA nucleic acids.

TABLE 2

TABLE 3 part I

part II

1 Propidium Iodide 2 CD3 3 CD4 4 CD8 5 CD10 6 CD13 7 CD19 8 CD20 9 CD2610 CD29 11 CD38 12 CD44 13 CD49d 14 CD54 15 CD58 16 CD80 17 CD138

Supplementary Table CMP prop cd3 cd4 cd8 cd10 cd13 cd19 cd20 cd26 cd29cd38 cd44 cd49d cd54 cd58 cd80 cd138 freq. 1 0 0 0 0 0 0 0 0 0 1 0 0 0 00 0 0 24.087 2 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 1 6.671 3 0 0 0 0 0 0 0 00 1 0 0 0 1 0 0 0 5.935 4 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 5.623 5 0 00 0 0 0 0 0 1 1 0 0 0 0 0 0 0 5.271 6 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 04.779 7 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 0 4.434 8 0 0 0 0 0 0 0 0 0 1 01 0 0 0 0 0 4.074 9 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 3.831 10 0 0 0 0 00 0 0 0 0 0 0 0 1 0 0 0 3.576 11 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 3.50112 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2.522 13 0 0 0 0 0 0 0 0 0 1 0 1 01 0 0 0 2.383 14 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 1.776 15 0 0 0 0 0 00 0 1 0 0 0 0 1 0 0 0 1.686 16 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 1.57217 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1.540 18 0 0 1 0 0 0 0 0 0 0 0 0 00 0 0 0 1.387 19 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1.360 20 0 0 0 0 0 00 0 1 1 0 0 1 1 0 0 1 1.322 21 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 1.31722 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0 0 0 1.276 23 0 0 0 0 0 1 0 0 0 1 0 0 00 0 0 0 1.220 24 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 1 1.069 25 0 0 0 0 0 00 0 0 0 1 1 0 0 0 0 0 1.068 26 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1.03827 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 955 28 0 0 0 0 0 0 0 0 0 1 0 0 0 11 0 0 886 29 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 875 30 0 0 0 0 0 0 0 0 00 0 1 0 1 0 0 0 873 31 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 865 32 0 0 1 00 0 0 0 0 1 0 0 0 1 0 0 0 815 33 0 0 0 0 0 1 0 0 1 1 0 0 0 1 0 0 1 80634 0 0 1 0 0 0 0 0 0 1 0 1 0 1 0 0 0 784 35 0 0 0 0 0 1 0 0 1 1 0 0 1 11 0 1 761 36 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 747 37 0 0 0 0 0 0 0 0 11 0 0 0 1 1 0 1 726 38 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 713 39 0 0 0 00 0 0 0 1 1 1 0 0 0 0 0 0 697 40 0 0 1 0 0 0 0 0 0 1 0 0 1 0 0 0 0 67841 0 0 1 0 0 0 0 0 0 1 0 1 1 1 0 0 0 665 42 0 0 0 0 1 0 0 0 1 0 1 0 0 00 0 0 640 43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 617 44 0 0 0 0 0 0 0 0 01 1 1 0 0 0 0 0 586 45 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 581 46 0 0 0 00 0 0 0 1 1 0 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1. A method for treating a cancerous and/or an inflammatory disease in apatient, comprising internally administering to the patient an effectiveamount of a pharmaceutical preparation blocking the biological activityof at least one protein cluster (CMP) or group of CMPs containing atleast CD26 and/or CD29.
 2. The method according to claim 1 wherein thepatient is a human and/or an animal.
 3. The method according to claim 1wherein the disease is prostate cancer.
 4. The method according to claim1 wherein the pharmaceutical preparation is administered if a proteincluster (CMP) or a group of CMPs also containing CD44 and/or CD54 and/orCD138 and lacking at least one of CD3, CD4, CD8, CD1O, CD13, CD19, CD20,CD38, CD49d, CD58, and CD80 is identified on cell surfaces of cellsobtained from an affected part of the body of the patient.
 5. The methodaccording to claim 3 wherein said cells are obtained from a tissue blockand/or a single tissue section, the tissue being removed from theprostate of the patient.
 6. The method of claim 1, further comprisingthe step of using a pharmaceutical preparation blocking the biologicalactivity of at least one protein cluster (CMP) or group of CMPscontaining at least CD26 and/or CD29 for the treatment of a cancerousand/or an inflammatory disease in a patient by internally administeringto the patient suffering such disease the pharmaceutical preparation. 7.Use of a pharmaceutical preparation blocking the biological activity ofat least one protein cluster (CMP) or group of CMPs containing at leastCD26 and/or CD29 for the preparation of a medicament for the treatmentof a cancerous and/or an inflammatory disease in a patient.
 8. Apharmaceutical composition for the treatment of a cancerous and/or aninflammatory disease in a patient comprising a pharmaceuticalpreparation blocking the biological activity of at least one proteincluster (CMP) or group of CMPs containing at least CD26 and/or CD29. 9.The pharmaceutical composition according to claim 8 wherein thecancerous disease is prostate cancer.
 10. The pharmaceutical compositionaccording to claim 8 wherein said pharmaceutical preparation comprisesan antibody, preferably a monoclonal antibody, and/or a proteincross-linking agent and/or at least one of TSPAN4, CD9, Filamin, FLNB,CD81, CD46, MAP4K4, FHL2, NME1, PKC alpha, YWHAB, ITGB1BP1, LGALS8 andGNB2L1.
 11. The pharmaceutical composition of claim 8 further comprisinga pharmaceutically acceptable carrier.
 12. The pharmaceuticalcomposition claim 8, which is formulated for oral, parenteral,intravenous, intramuscular, buccal, transdermal or transmucosal route ofadministration, in immediate release form or in controlled release form.13. A method for identifying a cancerous and/or an inflammatory diseasein a patient comprising at least the step of examining if at least aprotein cluster (CMP) or a group of CMPs containing at least CD26 and/orCD29 can be identified on the cell surfaces of cells from a part of thebody of the patient, wherein said part is suspected to be affected bysaid disease.
 14. The method according to claim 13 wherein at least oneprotein cluster (CMP) or group of CMPs also containing CD44 and/or CD54and/or CD138 and lacking at least one of CD3, CD4, CD8, CD1O, CD13,CD19, CD20, CD38, CD49d, CD58, and CD80 is identified on the cellsurfaces of said cells.
 15. The method according to claim 13 wherein atleast one protein cluster (CMP) or group of CMPs lacking at least one ofCD3, CD4, CD8, CD1O, CD13, CD19, CD20, CD38, CD49d, CD58, CD80, CD44,CD54, and/or CD138 is identified on the cell surfaces of said cells. 16.The method according to claim 13 wherein the disease is identified asprostate cancer if the cells derive from stroma and/or neoplasticepithelium of acini of prostate tissue and/or if at least 70%,preferably at least 75%, of the CMPs on the cell surface of at least onecell contain CD26 and/or CD29 and/or if at least 20%, preferably atleast 35%, of the CMPs on the cell surface of at least one cell compriseCD26 and/or CD29 and lack at least CD3, CD4, CD8, CD1O, CD13, CD19,CD20, CD38, CD49d, CD58, and CD80.
 17. A method of identifying at leastone candidate for development of anti-cancerous or anti-inflammatoryagents, comprising at least the step of examining if at least oneprotein cluster (CMP) or a group of CMPs containing at least CD26 and/orCD29 can be identified on the cell surfaces of cells from a part of thebody of the patient, wherein said part of the body is suspected to beaffected by a cancerous and/or inflammatory disease.
 18. The methodaccording to claim 17 wherein said part of the body is prostate tissueand the disease is prostate cancer.
 19. The method according to claim 17wherein at least one protein cluster (CMP) or group of CMPs alsocontaining CD44 and/or CD54 and/or CD138 and lacking at least one ofCD3, CD4, CD8, CD1O, CD13, CD19, CD20, CD38, CD49d, CD58, and CD80 isidentified on the cell surfaces of said cells.
 20. Use of a human and/oranimal antibody, preferably a monoclonal antibody, directed against atleast CD26 and/or CD29 for preparing a pharmaceutical preparation ormedicament for the treatment of prostate cancer.
 21. Composition or kitcomprising at least one antibody and/or at least one ligand wherein theantibody and/or ligand binds at least one cell surface protein selectedfrom the group of CD3, CD4, CD8, CD1O, CD13, CD19, CD20, CD26, CD29,CD38, CD44, CD49d, CD54, CD58, CD80 and CD138 and wherein the antibodyand/or ligand is coupled with a label.
 22. The composition or kitaccording to claim 21 wherein at least one label is a fluorescent dye,quantum dot, radioactive tag, spin label, binding tag for a secondantibody and/or an enzyme.
 23. The composition or kit according to claim21 for use in a method for identifying a cancerous and/or aninflammatory disease in a patient.
 24. The method of claim 13, furthercomprising the step of providing biochip wherein at least one surface ofthe biochip comprises antibodies and/or ligands binding to a proteincluster (CMP) or a group of CMPs of cell surfaces of human and/or animalcells, wherein the CMP contains at least CD26 and/or CD29.
 25. Themethod according to claim 24 wherein at least one surface of the biochipcontains antibodies and/or ligands binding to a protein cluster (CMP) ora group of CMPs of cell surfaces of human and/or animal cells, whereinthe CMP contains at least one of CD3, CD4, CD8, CD1O, CD13, CD19, CD20,CD38, CD44, CD49d, CD54, CD58, CD80, and CD138.